changed default aligner to giza (more reliable)
changed default aligner to giza (more reliable)

bugfix: test for sameness of source file when creating symlink for
SAMT step

hadoop cluster rollout:
- extended sleep times
- added some error checking for running processes

fhieber/incubator-joshua,kpu/joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,lukeorland/joshua,lukeorland/joshua,kpu/joshua,thammegowda/incubator-joshua,lukeorland/joshua,fhieber/incubator-joshua,lukeorland/joshua,fhieber/incubator-joshua,gwenniger/joshua,fhieber/incubator-joshua,gwenniger/joshua,kpu/joshua,lukeorland/joshua,lukeorland/joshua,gwenniger/joshua,fhieber/incubator-joshua,lukeorland/joshua,fhieber/incubator-joshua,thammegowda/incubator-joshua,thammegowda/incubator-joshua,gwenniger/joshua,gwenniger/joshua,thammegowda/incubator-joshua,lukeorland/joshua,kpu/joshua,fhieber/incubator-joshua,thammegowda/incubator-joshua,thammegowda/incubator-joshua,thammegowda/incubator-joshua,kpu/joshua,thammegowda/incubator-joshua,kpu/joshua,lukeorland/joshua,fhieber/incubator-joshua,gwenniger/joshua,thammegowda/incubator-joshua